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Ōmura is a castle town, and was the capital of Ōmura Domain, ruled by the local Ōmura clan for over 900 years in pre-Meiji Japan. It was the site of considerable foreign trade and missionary activity during the late Muromachi period, and the Catholic saintMarina de Omura hails from this city. Due to its proximity to the trading settlement at Dejima in Nagasaki, was one of the first areas of Japan to re-open to foreign contact after the end of the national seclusion policy after the Meiji Restoration. In the opera Madama Butterfly, set in nearby Nagasaki, the place name Omara in the line "ed alla damigella Butterfly del quartiere d'Omara Nagasaki" probably refers to Ōmura. From 1868-1945, Ōmura was host to numerous military facilities as part of the Sasebo Naval District, most notably that of a major air base for the Imperial Japanese Navy Air Service. The former naval base was the location of the squalid[2]Ōmura Migrant Detention Center, where mainly Korean refugees—termed "stowaways" (mikkōsha synonymous with "smuggler")—were held until deportation, frequently for several years. Since August 1996 the nearby Ōmura Immigration Reception Center in a modern building serves the same function.[3]

The modern city was founded on February 11, 1942. It was largely destroyed by American bombing on October 25, 1944. Its postwar recovery was assisted by the construction of Nagasaki airport offshore in Ōmura Bay, and by other public works projects.

^"East Asian version of the Nazi concentration camps ... We should not be misled by the facts that it has no gas chambers ..." Hayashi Kōzō, cit. in: Morris-Suzuki, Tessa; Borderline Japan: foreigners and frontier controls in the post-war era; Cambridge 2010; ISBN978-0-521-86460-2, p. 167